[PyMOL] How to display .mtz files and work with them

[Matthias H. <mat...@ho...>]

Dear all,

I am having some trouble working with PyMOL and the new feature of loading and displaying .mtz files.
Sorry for the number of questions (and sorry if most seem trivial...), but I couldn't find the answers in the PyMOLWiki and not in the Schrodinger documentations.

PyMOL Version is 1.5.0.5 and it's running on Win7 Prof 64 bit.

1.) When loading a .mtz file, you start with the new volume representation. Options for color gradients, sigma levels, etc. are displayed in a nice graph in the command line window - but the command line is gone and I don't get any feedback about commands I write in PyMOL. How do I turn this graphical representation of the sigma levels & color gradients on and off?
2.) The volume is represented for one unit cell - and for one unit cell only. I would like to display the density just around one molecule in the unit cell or around a symmetry mate OUTSIDE the unit cell - which is the command to do so? Things like "map_trim" don't work (which is not a surprise - I am obviously not displaying a map as one used to do in the older PyMOL versions). You can't align the "group", which is created by loading a .mtz file to a selection or molecule by using the drop down menus or I couldn't find any other way to limit the map to one molecule or one chain in of my .pdb file. Any help on this is greatly appreciated.

3.) What I basically want to do (in other words): Open a .pdb file. Open a .mtz file. Display the electron density at 2.0 sigma around one specific chain or around one specific symmetry mate of my molecule. Can't be that difficult, can it? ;-)

Many thanks for any help!

Matthias